Publications by authors named "Stéphane Ranque"

139 Publications

Species Identification and In Vitro Antifungal Susceptibility of / Species Isolated from Clinical Respiratory Samples: A Multicenter Study.

J Fungi (Basel) 2022 Jun 29;8(7). Epub 2022 Jun 29.

Unité de Parasitologie-Mycologie, Département Prévention, Diagnostic, Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (AP-HP), 94000 Créteil, France.

spp. are emerging fungal pathogens, where and are the most reported species. Taxonomic and phylogenetic revisions in this genus have shown that represents a species complex, whereas is related to another genus called . The aims of this study were to identify clinical isolates of spp. at the species level, and to determine their antifungal susceptibility profiles. 70 clinical spp. isolates were identified by MALDI-TOF Mass Spectrometry (MS) and by multilocus rDNA genes sequencing including ITS and the D1/D2 genes. Among the 70 spp. isolates, 28 were identified as , 26 as , and 16 as . For antifungal susceptibility testing, Minimal Inhibitory Concentrations (MICs) or Minimal Effective Concentrations (MECs) were determined for 8 antifungals. All isolates had high MICs and MECs of amphotericin B and echinocandins, respectively, unlike and . For azole drugs, MICs were molecule- and species- dependent. The differences in in vitro susceptibility to antifungals underline the importance of accurate species identification. The MALDI-TOF MS can be a good alternative in routine laboratory to ensure fast identification of spp. and .
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http://dx.doi.org/10.3390/jof8070684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9321559PMC
June 2022

Cryptococcal Meningitis in Kidney Transplant Recipients: A Two-Decade Cohort Study in France.

Pathogens 2022 Jun 17;11(6). Epub 2022 Jun 17.

Centre de Recherche Saint-Antoine, CRSA, Inserm, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, Sorbonne Université, 75012 Paris, France.

Cryptococcosis is the third most common cause of invasive fungal infection in solid organ transplant recipients and cryptococcal meningitis (CM) its main clinical presentation. CM outcomes, as well as its clinical features and radiological characteristics, have not yet been considered on a large scale in the context of kidney transplantation (KT). We performed a nationwide retrospective study of adult patients diagnosed with cryptococcosis after KT between 2002 and 2020 across 30 clinical centers in France. We sought to describe overall and graft survival based on whether KT patients with cryptococcosis developed CM or not. Clinical indicators of CNS involvement and brain radiological characteristics were assessed. Eighty-eight cases of cryptococcosis were diagnosed during the study period, with 61 (69.3%) cases of CM. Mortality was high (32.8%) at 12 months (M12) but not significantly different whether or not patients presented with CM. Baseline hyponatremia and at least one neurological symptom were independently associated with CM ( < 0.001). Positive serum cryptococcal antigen at diagnosis was also significantly associated with CM ( < 0.001). On magnetic resonance imaging (MRI), three patterns of brain injury were identified: parenchymal, meningeal, and vascular lesions. Although CM does not affect graft function directly, it entails a grim prognosis.
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http://dx.doi.org/10.3390/pathogens11060699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9227085PMC
June 2022

Outbreak of central nervous system infections among children in Thai Binh, Viet Nam.

Emerg Microbes Infect 2022 Dec;11(1):1683-1692

IHU-Méditerranée Infection, Marseille, France.

From July to October 2020, 99 cases of central nervous system (CNS) infections were identified in Thai Binh Pediatric Hospital, Viet Nam, representing a five-fold increase compared to the baseline incidence during the previous five years. Clinical data were retrospectively collected. Cerebrospinal fluid specimens (CSF) were secondarily tested for pathogens using viral culture and PCR assays. Patient median age was 5 years (0-12 years); 58.6% were male. Of these children, 83.8% had CSF white blood culture (WBC) counts of ≥ 10 cells/µL, including 58 of 99 (58.6%) with a WBC count ≥ 100 cells/µL. Overall, 72 (72.7%) patients had confirmed infections with a pathogen identified in the CSF, the majority of which (66) were enterovirus. Sequencing results suggested that the rise of incidence observed in 2020 was due to Echovirus 4 ( =  45), Echovirus 30 ( =  8), and Echovirus 6 (=  1) circulation. A confirmed CNS infection was significantly associated with older age (≥5 years, OR = 3.64,  = 0.03) and with an increased WBC count in the CSF (OR = 6.38, -value = 0.01 for WBCs from 10 to <100 and OR = 7.90, -value = 0.002 for WBCs ≥100). Ninety-seven (97) of 99 (98.0%) children received empiric antimicrobial treatment, and 35 (35.3%) were treated with multiple antibiotics. Eighty-four (84) patients (84.9%) were discharged home, and 11 (11.1%) were transferred to the National Hospital because their condition had worsened. No deaths were recorded. Point-of-care tests, including real-time PCR assays to identify common pathogens, should be implemented for more accurate diagnosis and more appropriate antibiotic use.
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http://dx.doi.org/10.1080/22221751.2022.2088405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9225704PMC
December 2022

Pericardial Effusion Due to : A Case Report and Review of the Literature.

Pathogens 2022 May 20;11(5). Epub 2022 May 20.

Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France.

Invasive infections due to spp. are life-threatening opportunistic fungal infections that may affect a wide array of organs. Here, we described a case of pericardial effusion due to &nbsp; in a 42-year-old female after a heart transplantation. was isolated from the pericardial fluid, pericardial drain hole and the swab of the sternal surgery scar wound. The late mycological diagnosis due to blood culture negative, the ineffective control of pulmonary bacterial infection and the late start antifungal therapy were the contributing factors in the patient's death.
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http://dx.doi.org/10.3390/pathogens11050598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145057PMC
May 2022

Identification of a clonal population of Aspergillus flavus by MALDI-TOF mass spectrometry using deep learning.

Sci Rep 2022 01 28;12(1):1575. Epub 2022 Jan 28.

AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, 75013, Paris, France.

The spread of fungal clones is hard to detect in the daily routines in clinical laboratories, and there is a need for new tools that can facilitate clone detection within a set of strains. Currently, Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry is extensively used to identify microbial isolates at the species level. Since most of clinical laboratories are equipped with this technology, there is a question of whether this equipment can sort a particular clone from a population of various isolates of the same species. We performed an experiment in which 19 clonal isolates of Aspergillus flavus initially collected on contaminated surgical masks were included in a set of 55 A. flavus isolates of various origins. A simple convolutional neural network (CNN) was trained to detect the isolates belonging to the clone. In this experiment, the training and testing sets were totally independent, and different MALDI-TOF devices (Microflex) were used for the training and testing phases. The CNN was used to correctly sort a large portion of the isolates, with excellent (> 93%) accuracy for two of the three devices used and with less accuracy for the third device (69%), which was older and needed to have the laser replaced.
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http://dx.doi.org/10.1038/s41598-022-05647-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8799650PMC
January 2022

Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus.

Viruses 2021 12 16;13(12). Epub 2021 Dec 16.

Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, France.

Background: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses.

Methods: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute.

Results: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant.

Conclusions: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.
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http://dx.doi.org/10.3390/v13122528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709236PMC
December 2021

Real-Time PCR Assay for the Detection of Dermatophytes: Comparison between an In-House Method and a Commercial Kit for the Diagnosis of Dermatophytoses in Patients from Dakar, Senegal.

J Fungi (Basel) 2021 Nov 10;7(11). Epub 2021 Nov 10.

IHU Méditerranée Infection, 13005 Marseille, France.

Background: PCR assays have been developed for the diagnosis of dermatophytes, yet data in African populations are scarce.

Objective: This study aimed to compare two PCR assays for the diagnosis of dermatophytosis in outpatients at the Aristide Le Dantec University Hospital in Dakar, Senegal.

Patients And Methods: A total of 105 samples, including 24 skin, 19 nail and 62 hair samples collected from 99 patients were included in this study. Each sample was subjected to conventional diagnosis (CD), including direct microscopy and culture, and two real-time PCR assays: one in-house (IH)-PCR, used at the University Hospital of Marseille and the Eurobio Scientific commercial kit (CK): designed for the specific detection of six dermatophytes not including .

Results: Of the 105 specimens, 24.8%, 36.2% and 20% were positive by CD, IH-PCR and CK-PCR, respectively. The IH-PCR and CK-PCR exhibited 88.9% and 65.4% sensitivity, respectively. With a 36.6 diagnostic odd ratio and 1.41 needed to diagnose, the IH-PCR displayed better diagnostic indices than the CK-PCR. It is notable that, when considering the species that it claims to detect, when it came to skin and nail samples, CK-PCR sensitivity increased to 77%.

Conclusions: The pan-dermatophyte IH-PCR performed better in the diagnosis of dermatophytosis in this African population than the CK-PCR, which is not designed to detect . Nevertheless, both assays exhibited similarly good diagnostic indices for tinea corporis and tinea unguium, both of which are localisations where is more rarely involved than in tinea capitis.
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http://dx.doi.org/10.3390/jof7110949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8624614PMC
November 2021

Chronic Diseases Associated with Yeast.

J Fungi (Basel) 2021 Oct 12;7(10). Epub 2021 Oct 12.

Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.

are a lipid-dependent basidiomycetous yeast of the normal skin microbiome, although DNA has been recently detected in other body sites and has been associated with certain chronic human diseases. This new perspective raises many questions. Are these yeasts truly present in the investigated body site or were they contaminated by other body sites, adjacent or not? Does this DNA contamination come from living or dead yeast? If these yeasts are alive, do they belong to the resident mycobiota or are they transient colonizers which are not permanently established within these niches? Finally, are these yeasts associated with certain chronic diseases or not? In an attempt to shed light on this knowledge gap, we critically reviewed the 31 published studies focusing on the association of spp. with chronic human diseases, including psoriasis, atopic dermatitis (AD), chronic rhinosinusitis (CRS), asthma, cystic fibrosis (CF), HIV infection, inflammatory bowel disease (IBD), colorectal cancer (CRC), and neurodegenerative diseases.
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http://dx.doi.org/10.3390/jof7100855DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8540640PMC
October 2021

: A Selective Culture Medium for Species.

J Fungi (Basel) 2021 Oct 1;7(10). Epub 2021 Oct 1.

Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille (AP-HM), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées (SSA), VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.

species are fastidious and slow-growing yeasts in which isolation from polymicrobial samples is hampered by fast-growing microorganisms. selective culture media are needed. Although cycloheximide is often used, some fungi, including the chief human commensal , are resistant to this compound. This study aimed to test whether the macrolide rapamycin could be used in combination with cycloheximide to develop a -selective culture medium. Rapamycin susceptibility testing was performed via microdilution assays in modified Dixon against two and five spp. The MIC was the lowest concentration that reduced growth by a minimum of 90%. Rapamycin ± cycloheximide 500 mg/L was also added to FastFung solid, and yeast suspensions were inoculated and incubated for 72 h. Rapamycin MICs for spp. ranged from 0.5 to 2 mg/L, except for , for which the MIC was >32 mg/L. stains were rapamycin-resistant. Rapamycin and cycloheximide supplementation of the FastFung medium effectively inhibited the growth of non- yeast, including cycloheximide-resistant and . Based on our findings, this "" medium should be further evaluated on polymicrobial samples for isolation and culture.
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http://dx.doi.org/10.3390/jof7100824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8538348PMC
October 2021

Spatiotemporal Dynamic of the RTS,S/AS01 Malaria Vaccine Target Antigens in Senegal.

Am J Trop Med Hyg 2021 10 11;105(6):1738-1746. Epub 2021 Oct 11.

Department of Parasitology and Mycology, Cheikh Anta Diop University, Dakar, Senegal.

The RTS,S/AS01 malaria vaccine confers only moderate protection against malaria. Evidence suggests that the effectiveness of the RTS,S/AS01 vaccine depends upon the parasite population genetics, specifically regarding the circumsporozoite protein haplotypes in the population. We investigated Plasmodium falciparum circumsporozoite protein (PfCSP) gene sequences from two endemic sites in 2018 in Senegal. The PfCSP sequences were compared with those retrieved from the Pf3k genome database. In the central repeat region of PfCSP, the distribution of haplotypes differed significantly between the two study sites (Fisher's exact test, P < 0.001). No 3D7 vaccine strain haplotype was observed in this locus. In the C-terminal region, there was no significant difference in haplotypes distribution between Kedougou and Diourbel (Fischer's exact test, P = 0.122). The 3D7 haplotype frequency was 8.4% in early samples (2001-2011), but then it contracted in the subsequent years. The extensive plasticity of the P. falciparum genes coding the RTS,S/AS01 vaccine target antigens may influence the immune responses to circulating alleles. Monitoring the genetic diversity baseline and its dynamics over time and space would be instrumental in rationally improving the malaria RTS,S/AS01 vaccine and/or its implementation schedule.
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http://dx.doi.org/10.4269/ajtmh.21-0369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8641351PMC
October 2021

"Chiclero's Ulcer" Due to in Travelers Returning from Central America: A Case Report and Review of the Literature.

Pathogens 2021 Aug 31;10(9). Epub 2021 Aug 31.

Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France.

Cutaneous leishmaniasis (CL) due to a New World species of Leishmania is increasingly seen among returning international travelers, and most cases arise from travel to Mexico, Central and South America. We described a case of CL in a women presenting a nonhealing ulceration under her right ear with slight increase of size of the left parotid gland under the skin lesion, evolving for 4 months. In her history of travel, she reported a ten-day stay in Mexico during the Christmas vacation in the Yucatan region with only half a day walking in the tropical forest. Diagnosis of CL due to was done via PCR detection and sequencing from swab sampling of the lesion. The patient recovered without antiparasitic treatment. Clinicians should consider diagnosing Chiclero's ulcer in patients returning from endemic areas such as Central America and Texas who present with chronic ulceration. A noninvasive sampling is sufficient for the PCR-based diagnosis of this disease.
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http://dx.doi.org/10.3390/pathogens10091112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8469509PMC
August 2021

Antifungal Susceptibility of 182 Fusarium Species Isolates from 20 European Centers: Comparison between EUCAST and Gradient Concentration Strip Methods.

Antimicrob Agents Chemother 2021 11 20;65(12):e0149521. Epub 2021 Sep 20.

AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, Paris, France.

We determined the susceptibility of 182 Fusarium species isolates to five antifungal drugs (amphotericin B, voriconazole, posaconazole, isavuconazole, and terbinafine) by the EUCAST method. Based on the latest taxonomic insights, isolates collected from 20 European centers were distributed into seven complexes and 27 species. The susceptibility was variable, depending on the species. Comparison with the gradient concentration strip method, which was used for 77 isolates, showed essential agreement values for voriconazole, posaconazole, isavuconazole, and amphotericin B of 17%, 91%, 83%, and 70%, respectively.
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http://dx.doi.org/10.1128/AAC.01495-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8597759PMC
November 2021

and Snail Infestations by the Group in Niakhar, Senegal.

Pathogens 2021 Jul 8;10(7). Epub 2021 Jul 8.

Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France.

Thorough knowledge of the dynamics of spp. infestation could help to control the spread of schistosomiasis. This study describes the spatio-temporal dynamics of and infestation by the group of blood flukes in Niakhar, Senegal. Molecular identification of the group was performed by real-time PCR, targeting the Dra 1 gene in 810 samples of spp. collected during the schistosomiasis transmission season in 2013. In addition to Dra 1 PCR, a rapid diagnostic-PCR was performed on a sub-group of 43 snails to discriminate , , and Out of 810 snails, 236 (29.1%) were positive for Dra 1 based on the PCR, including 96.2% and 3.8% of and respectively. Among the sub-group, 16 samples were confirmed to be while one was identified as a mixture of and . Snails infestations were detected in all villages sampled and infestation rates ranged from 15.38% to 42.11%. The prevalence of infestation was higher in the north (33.47%) compared to the south (25.74%). Snail populations infestations appear early in the rainy season, with a peak in the middle of the season, and then a decline towards the end of the rainy season. Molecular techniques showed, for the first time, the presence of in the spp. population of Niakhar. The heterogeneity of snail infestations at the village level must be taken into account in mass treatment strategies. Further studies should help to improve the characterizations of the schistosome population.
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http://dx.doi.org/10.3390/pathogens10070860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8308860PMC
July 2021

Detection of in Hospitalized Children Less Than 3 Years of Age.

J Fungi (Basel) 2021 Jul 9;7(7). Epub 2021 Jul 9.

Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France.

Few data are available in the literature regarding infection in children under 3 years old. This retrospective cohort study aimed to describe medically relevant information among them. All children under 3 years old treated in the same medical units from April 2014 to August 2020 and in whom a evaluation was undertaken were enrolled in the study. A positive case was defined as a child presenting at least one positive PCR for in a respiratory sample. Medically relevant information such as demographical characteristics, clinical presentation, microbiological co-infections, and treatments were collected. The objectives were to describe the characteristics of these children with colonization/infection to determine the key underlying diseases and risk factors, and to identify viral respiratory pathogens associated. The PCR was positive for in 32 children. Cardiopulmonary pathologies (21.9%) were the most common underlying disease in them, followed by severe combined immunodeficiency (SCID) (18.8%), hyaline membrane disease (15.6%), asthma (9.4%) and acute leukaemia (6.3%). All SCID children were diagnosed with pneumonia. Co-infection with Pj/Rhinovirus (34.4%) was not significant. Overall mortality was 18.8%. Paediatric is not restricted to patients with HIV or SCID and should be considered in pneumonia in children under 3 years old.
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http://dx.doi.org/10.3390/jof7070546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8306698PMC
July 2021

Meningoencephalitis with refractory intracranial hypertension : Consider Decompressive craniectomy.

J Neurosurg Sci 2021 Aug 3. Epub 2021 Aug 3.

Department of Neurosurgery, Aix Marseille Univ, APHM, UH Timone, Marseille, France.

Background: The benefits of decompressive craniectomy (DC) have been demonstrated in malignant ischemic stroke and traumatic brain injuries with refractory intracranial hypertension (ICH) by randomized controlled trials. Some reports advocate the potential of DC in the context of ICH due to meningoencephalitis (ME) with focal cerebral edema but its interest remains controversial especially when there is diffuse cerebral edema. The aim of this study is to assess the benefits of DC in meningoencephalitis with malignant cerebral edema whether it is focal or diffuse.

Methods: We report two cases successfully treated in our instution, plus we conducted a systematic literature review focused on cases of DC in ME in compliance with prisma guidelines.

Results: the first patient is a 36-years-old woman who suffered from fulminant pneumococcal meningoencephalitis (ME) with refractory ICH following a transphenoidal removal of pituitary adenoma. The second patient is a 20-years-old man suffering from neuromeningeal cryptococcosis with refractory ICH. In both cases DC led to major clinical improvement with a GOS-E 8 at one year. These results are consistent with the literature review which reports a favorable outcome in 85% of cases.

Conclusions: DC appears to be a promising therapeutic option in cases of ME with refractory ICH. Thus, reliable criteria will have to be defined to guide us in our practice in emergency cases where DC has not been part of the therapeutic arsenal yet.
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http://dx.doi.org/10.23736/S0390-5616.21.05397-2DOI Listing
August 2021

Immunoblot for the Diagnosis of Cutaneous Leishmaniasis in French Guiana.

Am J Trop Med Hyg 2021 05 3;104(6):2091-2096. Epub 2021 May 3.

1Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, Centre Hospitalier Andrée Rosemon, Cayenne, French Guiana.

Cutaneous leishmaniasis (CL) is firmly established in South America. We aimed to assess the detection of IgG antibodies against 14 and/or 16 kDa antigens by immunoblot (IB) for CL serological diagnosis in French Guiana, an area where many endemic pathogens could interfere with it. This study was performed retrospectively on sera from 141 patients at the Cayenne tertiary hospital: 30 were patients with confirmed CL, 71 were diagnosed with various other endemic pathogens, 11 were diagnosed with an autoimmune disease, and 29 controls had no history of CL. Antibodies bound to the 14 and/or 16 kDa antigens in 27 of the 30 CL patients' sera and in 39 of the 111 non-CL patients' sera (26 from the infectious diseases group, four from the autoimmune diseases group, and nine from the dermatology department). The method tested showed a high sensitivity (90%) and a low specificity (66%), and a diagnosis odds ratio of 17.5 (95% CI [4.6-78.0]). This IB may be helpful to exclude the diagnosis of CL, prompting physicians to look for another diagnosis in the case of a negative IB.
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http://dx.doi.org/10.4269/ajtmh.19-0591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176500PMC
May 2021

Evaluation of 11 DNA Automated Extraction Protocols for the Detection of the 5 Mains Candida Species from Artificially Spiked Blood.

J Fungi (Basel) 2021 Mar 19;7(3). Epub 2021 Mar 19.

Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France.

The molecular detection of plays an important role in the diagnosis of candidaemia, a major cause of morbidity and mortality. The sensitivity of this diagnosis is partly related to the efficiency of yeast DNA extraction. In this monocentric study, we investigated the suitability of 11 recent automated procedures for the extraction of low and high amounts of DNA from spiked blood. The efficacy of the DNA extraction procedures to detect spp. in blood samples ranged from 31.4% to 80.6%. The NucliSENS easyMAG procedure was the most efficient, for each species and each inoculum. It significantly outperformed the other procedures at the lower inocula mimicking the clinical setting. This study highlighted a heterogeneity in DNA extraction efficacy between the five main species (, , , and ). Up to five automated procedures were appropriate for DNA extraction, whereas only one method yielded an appropriate detection of low amount of . In the era of the syndromic approach to bloodstream infection diagnosis, this evaluation of 11 automated DNA extraction methods for the PCR diagnosis of candidaemia, puts the choice of an appropriate method in routine diagnosis within the reach of laboratories.
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http://dx.doi.org/10.3390/jof7030228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003619PMC
March 2021

Clinical Origin and Species Distribution of spp. Isolates Identified by Molecular Sequencing and Mass Spectrometry: A European Multicenter Hospital Prospective Study.

J Fungi (Basel) 2021 Mar 25;7(4). Epub 2021 Mar 25.

AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, 75013 Paris, France.

spp. are widespread environmental fungi as well as pathogens that can affect plants, animals and humans. Yet the epidemiology of human fusariosis is still cloudy due to the rapidly evolving taxonomy. The Mass Spectrometry Identification database (MSI) has been developed since 2017 in order to allow a fast, accurate and free-access identification of fungi by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the MSI database user network, we aim to study the species distribution of spp. isolates in an international multicenter prospective study. This study also allowed the assessment of the abilities of miscellaneous techniques to identify isolates at the species level. The identification was performed by PCR-sequencing and phylogenic-tree approach. Both methods are used as gold standard for the evaluation of mass spectrometry. Identification at the species complex was satisfactory for all the tested methods. However, identification at the species level was more challenging and only 32% of the isolates were correctly identified with the National Center for Biotechnology Information (NCBI) DNA database, 20% with the Bruker MS database and 43% with the two MSI databases. Improvement of the mass spectrometry database is still needed to enable precise identification at the species level of any isolates encountered either in human pathology or in the environment.
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http://dx.doi.org/10.3390/jof7040246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8064482PMC
March 2021

Occurrence of Ten Protozoan Enteric Pathogens in Three Non-Human Primate Populations.

Pathogens 2021 Mar 2;10(3). Epub 2021 Mar 2.

IHU Méditerranée infection, 13005 Marseille, France.

Non-human primate populations act as potential reservoirs for human pathogens, including viruses, bacteria and parasites, which can lead to zoonotic infections. Furthermore, intestinal microorganisms may be pathogenic organisms to both non-human primates and humans. It is, therefore, essential to study the prevalence of these infectious agents in captive and wild non-human primates. This study aimed at showing the prevalence of the most frequently encountered human enteric protozoa in non-human primate populations based on qPCR detection. The three populations studied were common chimpanzees () in Senegal and gorillas () in the Republic of the Congo and in the Beauval Zoo (France). spp. were mainly found, with an occurrence close to 100%, followed by (23.7%), (7.9%), (1.3%) and (0.2%). None of the following protozoa were detected: , , , . , or . As chimpanzees and gorillas are genetically close to humans, it is important to monitor them frequently against different pathogens to protect these endangered species and to assess potential zoonotic transmissions to humans.
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http://dx.doi.org/10.3390/pathogens10030280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001678PMC
March 2021

Pulmonary Madurella mycetomatis mycetoma secondary to knee eumycetoma, Senegal.

PLoS Negl Trop Dis 2021 03 25;15(3):e0009238. Epub 2021 Mar 25.

Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Dakar, Senegal.

Mycetoma is a neglected tropical disease which is endemic in Senegal. Although this subcutaneous mycosis is most commonly found on the foot, extrapodal localisations have also been found, including on the leg, knee, thigh, hand, and arm. To our knowledge, no case of blood-spread eumycetoma has been reported in Senegal. Here, we report a case of pulmonary mycetoma secondary to a Madurella mycetomatis knee eumycetoma. The patient was a 41-year-old farmer living in Louga, Senegal, where the Sudano-Sahelian climate is characterised by a short and unstable rainy season and a steppe vegetation. He suffered a trauma to the right more than 20 years previously and had received treatment for more than 10 years with traditional medicine. He consulted at Le Dantec University Hospital in Dakar for treatment of a right knee mycetoma which had been diagnosed more than 10 years ago. He had experienced a chronic cough for more than a year; tuberculosis documentation was negative. Grains collected from the knee and the sputum isolated M. mycetomatis, confirmed by the rRNA gene ITS regions nucleotide sequence analysis. An amputation above the knee was performed, and antibacterial and antifungal therapy was started with amoxicillin-clavulanic acid and terbinafine. The patient died within a month of his discharge from hospital.
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http://dx.doi.org/10.1371/journal.pntd.0009238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993608PMC
March 2021

Intra- and inter-laboratory comparison of mDixon and FastFung broths for Malassezia antifungal susceptibility testing.

Mycoses 2021 Jul 20;64(7):716-720. Epub 2021 May 20.

Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.

Background: Malassezia spp. antifungal susceptibility testing (AFST) capacities are limited by the lack of efficient and standardised AFST procedure, mainly because of the fastidious cultivation of these yeast.

Objectives: This study aimed to compare the FastFung broth (FFB) to modified Dixon broth (mDIXB) for the in vitro AFST of Malassezia spp. Fluconazole, ketoconazole, voriconazole and terbinafine MICs against a 19 Malassezia strains, including 6 M furfur, 4 M pachydermatis, 5 M sympodialis and 4 M slooffiae.

Methods: The essential agreement (EA) between the two assays, and the intra- and inter-laboratory agreement of each assay were assessed.

Results: The MIC data obtained in our study were comparable to those reported in the literature. FFB showed to enhance Malassezia growth and displayed 100% (±2-fold dilution) EAs demonstrating similar performances to mDIXB. In addition, the MIC data obtained by using the FFB were reproducible between laboratories with EAs ranging from 94.7% to 100%.

Conclusions: Therefore, FFB is a suitable alternative to mDXB for Malassezia spp. AFST.
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http://dx.doi.org/10.1111/myc.13270DOI Listing
July 2021

Eukaryotic and Prokaryotic Microbiota Interactions.

Microorganisms 2020 Dec 17;8(12). Epub 2020 Dec 17.

Aix-Marseille Université, Instiut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Vecteurs et Infections TROpicales et MEditerranéennes, 13005 Marseille, France.

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host's immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.
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http://dx.doi.org/10.3390/microorganisms8122018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7767281PMC
December 2020

Comparison of Three Skin Sampling Methods and Two Media for Culturing Yeast.

J Fungi (Basel) 2020 Dec 9;6(4). Epub 2020 Dec 9.

Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.

is a lipid-dependent commensal yeast of the human skin. The different culture media and skin sampling methods used to grow these fastidious yeasts are a source of heterogeneity in culture-based epidemiological study results. This study aimed to compare the performances of three methods of skin sampling, and two culture media for the detection of yeasts by culture from the human skin. Three skin sampling methods, namely sterile gauze, dry swab, and Transwab with transport medium, were applied on 10 healthy volunteers at 5 distinct body sites. Each sample was further inoculated onto either the novel FastFung medium or the reference Dixon agar for the detection of spp. by culture. At least one colony of spp. grew on 93/300 (31%) of the cultures, corresponding to 150 samplings. The positive culture rate was 67%, 18%, and 15% ( < 10), for samples collected with sterile gauze, Transwab, and dry swab, respectively. The positive culture rate was 62% and 38% ( < 0.003) by using the FastFung and the Dixon media, respectively. Our results showed that sterile gauze rubbing skin sampling followed by inoculation on FastFung medium should be implemented in the routine clinical laboratory procedure for spp. cultivation.
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http://dx.doi.org/10.3390/jof6040350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7770598PMC
December 2020

FastFung: A novel medium for the culture and isolation of fastidious fungal species from clinical samples.

J Microbiol Methods 2021 01 21;180:106108. Epub 2020 Nov 21.

Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France; IHU Méditerranée Infection, Marseille, France. Electronic address:

We developed a novel culture medium, referred to FastFung medium as suitable for the culture of clinical fungi, including fastidious ones, for both research and diagnostic studies. It is based on Schædler agar supplemented with many essential components for the growth of fastidious fungi. It also contains selective antibacterial agents for the inhibition of contaminant bacteria growth. In this preliminary study, the FastFung medium was compared to the gold standard Sabouraud medium for 98 fungal and 20 bacterial strains. The fungal strain positive culture rate was 100% vs. 95% and the bacterial strain inhibition was 100% vs. 20%, for the FastFung and Sabouraud media, respectively. When compared to the Sabouraud medium on 120 clinical samples, the FastFung medium displayed both a higher fungal colonies count, and a lower culture contamination rate. Storage at 4 °C for 4 weeks did not alter the FastFung culture medium performances for the six isolates of Candida, Cryptococcus, and Penicillium tested. These encouraging results suggest future development of using the FastFung medium in clinical mycology and in mycobiome characterization. Further prospective evaluation aiming at assessing whether implementing the FastFung medium in the routine workflow simplifies and strengthen fungal isolation capacities in the clinical laboratory is warranted.
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http://dx.doi.org/10.1016/j.mimet.2020.106108DOI Listing
January 2021

Tinea incognito: Primum non nocere.

Int J Infect Dis 2021 02 17;103:597-598. Epub 2020 Nov 17.

IHU-Méditerranée Infection, Marseille, France; Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.ijid.2020.11.136DOI Listing
February 2021

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic that Includes the Species Complex.

Phytopathology 2021 07 9;111(7):1064-1079. Epub 2021 Sep 9.

Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the community voiced near unanimous support for a concept of that represented a clade comprising all agriculturally and clinically important species, including the species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus into seven genera, including the FSSC described as members of the genus , with subsequent justification in 2018 based on claims that the 2013 concept of is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of including the FSSC. We reassert the practical and scientific argument in support of a genus that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus were recombined in genus , and nine others were renamed Here the global community voices strong support for the inclusion of the FSSC in , as it remains the best scientific, nomenclatural, and practical taxonomic option available.
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http://dx.doi.org/10.1094/PHYTO-08-20-0330-LEDOI Listing
July 2021

Molecular Detection of Microorganisms Associated with Small Mammals and Their Ectoparasites in Mali.

Am J Trop Med Hyg 2020 12 29;103(6):2542-2551. Epub 2020 Oct 29.

1Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France.

Small mammals are the natural reservoirs for many zoonotic pathogens. Using molecular tools, we assessed the prevalence of bacteria and protozoans in small mammals and their ectoparasites in Faladjè, Bougouni, and Bamoko, Mali. A total of 130 small mammals belonging to 10 different species were captured, of which 74 (56.9%) were infested by ectoparasites, including , , , sensu lato, and spp. nymphs. DNA of was found in 14/75 (18.7%), 6/48 (12.5%), and 3/7 (42.8%) small mammals from Faladjè, Bougouni, and Bamako, respectively. In Faladjè, DNA was detected in 31/68 (45.6%) of and 14/22 (63.6%) of . In Bougouni, it was found in 2/26 (7.7%) of and 10/42 (23.8%) of . The sequences of obtained from small mammals were close to those of , , and uncultured spp. In Faladjè, DNA was detected in 64.4% (29/45) of spp. ticks, 4.5% (2/44) of , 12.5% (1/8) of , and 1.5% (1/68) of . We found DNA of in from Faladjè and DNA of and in from Bougouni. The results of our study show that several small mammal species harbor and may serve as potential reservoirs of spp., likely to play a major role in the maintenance, circulation, and potential transmission of bacteria in Mali. The pathogenicity of these bacteria for humans or animals remains to be demonstrated.
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http://dx.doi.org/10.4269/ajtmh.19-0727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695096PMC
December 2020

Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.

Emerg Infect Dis 2020 09;26(9):2031-2038

Saprochaete clavata is a pathogenic yeast responsible for rare outbreaks involving immunocompromised patients, especially those with hematologic malignancies. During February 2016-December 2017, we diagnosed S. clavata infections in 9 patients (8 with fungemia), including 3 within 1 month, at a cancer center in Marseille, France. The patients (median age 58 years), 4 of 9 of whom had acute myeloid leukemia, were hospitalized in 3 different wards. Ten environmental samples, including from 2 dishwashers and 4 pitchers, grew S. clavata, but no contaminated food was discovered. The outbreak ended after contaminated utensils and appliances were discarded. Whole-genome sequencing analysis demonstrated that all clinical and environmental isolates belonged to the same phylogenetic clade, which was unrelated to clades from previous S. clavata outbreaks in France. We identified a dishwasher with a deficient heating system as the vector of contamination.
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http://dx.doi.org/10.3201/eid2609.200341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454083PMC
September 2020

Autochthonous liver cystic hydatid: Past or actual French shepherd's disease?

IDCases 2020 26;21:e00843. Epub 2020 May 26.

IHU-Méditerranée Infection, Marseille, France.

Autochthonous hydatidosis in France and western Europa are uncommon since the beginning of the 21st century. We report here an authentic indigenous cystic echinococcosis case in a French shepherd. The risk of remerging pathology should not be neglected and measures to interrupt parasite transmission are still relevant.
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http://dx.doi.org/10.1016/j.idcr.2020.e00843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264046PMC
May 2020
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